Mass spectrometer system and method for matrix-assisted laser desorption measurements

ABSTRACT

The system for analyzing multiple samples includes a plurality of portable of sample supports each for accommodating a plurality of samples thereon, and an identification mechanism for identifying each sample location on each of the plurality of sample supports. The mass spectrometer is provided for analyzing each of the plurality of samples when positioned within a sample receiving chamber, and a laser source strikes each sample with a laser pulse to desorb and ionize sample molecules. The support transport mechanism provided  provides for automatically inputting and outputting each of the sample supports from the sample receiving chamber of the mass spectrometer. A vacuum lock chamber receives the sample supports and maintains at least one of the sample supports within a controlled environment while samples on another of the plurality of sample supports are being struck with laser pulses. The computer is provided for recording test data from the mass spectrometer and for controlling the operation of the system.

Note that more than one reissue application has been field. Thisapplication is a continuation of reissue application Ser. No.09/038,324, filed on Mar. 11, 1998, issued as RE37485, the entirecontent of which is incorporated by reference herein.

FIELD OF THE INVENTION

The present invention relates to mass spectrometer systems useful forobtaining matrix-assisted laser desorption measurements. Moreparticularly, this invention is directed to an automated massspectrometer system for combining high sample throughput with highreliability.

BACKGROUND OF THE INVENTION

Matrix-assisted laser desorption and ionization (MALDI) is a relativelynew technique that allows very large molecules, such as DNA fragmentsand proteins, to be desorbed from a solid sample and ionized withoutsignificant decomposition. Coupled with mass spectrometry, thistechnique allows the molecular weights of biological polymers and otherlarge molecules, including industrial polymers, to be preciselydetermined. One version of MALDI is described in a 1991 article in RapidCommunications in Mass Spectrometry, Vol. 5, Pages 198-202. A massspectrometer suitable for obtaining highly reliable matrix-assistedlaser desorption measurements is described in U.S. Pat. 5,045,694.

Most MALDI applications to date have employed time-of-flight massspectrometers, although magnetic deflection, Fourier Transform ioncyclotron resonance, and quadrupole ion trap mass analyzers have alsobeen used. A liquid solution of the sample to be analyzed is mixed witha solution containing an appropriate matrix, and a small aliquot of thismixtures is deposited on the source of the mass spectrometer (inside avacuum system). A vacuum lock is generally utilized to avoid venting thevacuum system. Loading a sample typically requires from one to severalminutes, and the attention of a skilled operator. A diligent operatorshould theoretically be able to load and run a sample every five or tenminutes using such a system, but it is difficult to maintain such a rateover an extended period. U.S. Pat. 5,288,644 discloses one technique forreducing the required time. A plurality of samples are loaded onto thesolid surface of a disk, which is rotated by a stepper motor forpositioning each sample respectively for striking by a laser beam.

Further improvements in the loading of samples for the laser desorptionmass analysis are required for this analytical procedure to gain greateracceptance and significantly increase the use of this analytical tool.The disadvantages of the prior art overcome by the present invention,and an improved system is hereinafter disclosed for obtainingmatrix-assisted mass spectrometer measurements. The loading of thesamples is highly automated for achieving both high sample throughputand high reliability. The present invention has a wide range ofapplication, and may be used with various analytical methods.

SUMMARY OF THE INVENTION

The present invention provides a highly automated system for preparing,loading, and running samples by MALDI mass spectrometry. Each step inthe process may be controlled and monitored by a computer. All sampleprocessing and identification information is recorded along with themass spectra measurements, so that automated processing of the data maybe performed. The typical input to this system is a collection ofsamples in relatively crude or unprocessed form, and the output providesdirect answers to specific questions posed by the scientists relative tothe samples. This system is particularly useful in application thatrequire processing a large number of samples to provide the requireddata. Examples include DNA sequencing on the scale required by the HumanGenome Project, protein sequencing, and determination of the locationsand nature of post-translational modifications of proteins.

While there are many potential applications of this invention, the HumanGenome Project provides a particularly timely example of the need forthis advancement. The DNA that composes the human genome has about 3.5billion base pairs. Although highly developed techniques for sequencingDNA have been developed, at least a decade would be required usingavailable techniques to accurately sequence even one such DNA.Completion of the genome project will require sequencing thousands orpossibly millions of such genomes from both humans and other organisms.The present invention will accordingly be described in detail below withparticular emphasis on its application to DNA sequencing, but it shouldbe recognized that it has other applications.

It is an object of this invention to provide improved equipment andtechniques for performing MALDI mass spectrometry analysis. Theequipment and techniques of this invention substantially reduce both thetime and expertise required to load, run, and analyze multiple samples,thereby significantly reducing the cost of the analysis.

A significant feature of this invention relates to the effectivecombination of mass spectrometry equipment and techniques withmatrix-assisted laser desorption ionization equipment and techniques.The equipment and techniques may be utilized to substantially reduce thecost of DNA sequencing. The invention may also be used for determiningthe molecular weight of various large molecules, such as biological andindustrial polymers.

A significant advantage of this invention relates to the reduced timerequired for mass spectrometry analysis of multiple samples. Theinvention is particularly well suited for use with a time-of-flight massspectrometer.

These and further objects, features, and advantages of the presentinvention will become apparent from the following detailed description,wherein reference is made to the figures in the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts one embodiment of a sample holder according to thepresent invention for loading multiple samples for mass analysis.

FIG. 2 depicts an alternate embodiment of suitable apparatus for loadingmultiple samples for mass analysis.

FIG. 3 is a block diagram of an automated system for processing andpreparing samples, and for transferring multiple sample aliquots on asample plate to selected sample positions.

FIG. 4 is a top view of a suitable system for automatically transferringsample plates between a sample storage chamber and an ion source chamberof a mass spectrometer.

FIG. 5 is a front view of the system shown in FIG. 4.

FIG. 6 is a top view of a simplified vacuum lock assembly prior toloading a sample plate into the vacuum lock chamber.

FIG. 7 is a top view of the simplified vacuum lock assembly as shown inFIG. 6 after loading the sample plate into the analysis chamber.

FIG. 8 is a schematic diagram of a fully automated system according tothe present invention.

FIG. 9 is a schematic illustration of a matrix-assisted laser desorptionion source combined with a simplified representation of a massspectrometer according to the present invention.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

The system according to this invention typically involves manycomponents integrated under computer control into a fully automatedsystem. A typical system of ten primary components includes: (1) asample plate or other sample receiving surface upon which a large numberof physically separated and distinguishable samples can be loaded inliquid solution then allowed to dry; (2) identification means foruniquely identifying each sample position and sample plate; (3) anautomated system for processing and preparing samples and transferringaliquots to selected sample positions on a sample plate; (4) dryingmeans for storing one or more sample plates in a controlled environment;(5) transferring means for automatically or manually transferring aplurality of sample plates from the controlled environment into thesample receiving chamber of the MALDI mass spectrometer; (6) anautomated vacuum lock system for transferring sample plates between thereceiving chamber and the ionization source of the MALDI massspectrometer without significantly increasing the pressure in the massspectrometer vacuum system; (7) sequencing means for sequentiallyplacing each sample on the sample receiving surface in the path of thelaser beam, so that its MALDI spectrum is recorded and stored along withthe sample identification information; (8) means for automaticallyadjusting the laser intensity and sample position relative to the laserbeam to obtain MALDI spectra which meet or exceed predeterminedcriteria; (9) means for automatically calibrating the mass axis of theMALDI mass spectrometer; and (10) means for automatically interpretingthe MALDI mass spectra obtained from one or more samples to determineand produce the answer to a specific question. A scientist may thus makeinquiry as to the sequence of the bases in a particular DNA fragment,and the system of this invention will rapidly provide the answer in ahighly cost-effective manner.

In some applications manual operations may be substituted for thecorresponding automated step, but the full power and speed of theinvention is realized when operator intervention is required at most,once or twice per day. Each of the ten primary components (and/orcorresponding steps) which may comprise an exemplary system is describedin more detail below.

1. Sample Receiving Surface

A preferred embodiment of a sample receiving surface is illustrated inFIG. 1. The depicted sample plate 10 consists of a thin, substantiallysquare plate 12 of stainless steel or other suitable electricallyconducting material approximately 1.5 mm thick and 50 mm wide. The plate10 may contain precisely located holes to allow the position andorientation of the plate to be accurately determined relative to amoveable stage, which is required both in the sample loading step and inthe ion source of the mass spectrometer. The sample plate 10 alsocontains a plurality of precisely determinable sample positions 16 onthe upper sample receiving surface 18 of the plate. These samplepositions may be determined by a number of photoetched and numberedsample positions or wells as illustrated in FIG. 1. Alternatively, anumber of sample positions may be identified by electroplated samplespots and numbers on the surface 18 of the sample plate, with the sampleidentification providing the row and column number of a respectiveadjoining sample, i.e., position identification 34 being the sample inthe third row and the fourth column of the plurality of samples on theplate 10.

A plate 10 may thus contain 100 sample positions each identified by asample spot which is about 2.5 mm in diameter in a precisely knownlocation on the plate, with each sample support being suitable foraccepting a few microliters of sample solution. Each sample spot may befurther identified by a corresponding number similarly plated or etchedon the surface 18. Alternatively, the plate may contain a larger numberof spots in which photoetched sample wells or photoplated sample spotsof appropriate diameter in precisely known locations are prepared on thesample surface without the corresponding sample numbers on the surface.The known sample coordinates thus may be sufficient to identify eachsample well or spot. In the case of a 400 sample array (20 rows and 20columns), 2 mm sample wells or spots have been used successfully. For a1024 array (32 rows and 32 columns), a 50 mm square plate and 1 mmdiameter sample positions have been successfully used. Anotheralternative is to use a smooth unmodified sample plate in which the x-ycoordinates are sufficient to define a unique sample position. Thedetailed description of the invention discussed below utilizes 50 mmplates with square arrays of sample positions which can accommodate upto 1024 distinguishable sample positions. Any distribution of samplesover a surface, either known or unknown, can be accommodated. Sampleplates of a variety of geometries could be used, including circular,rectangular, and regular and irregular polygons. The maximum size of thesample plate is limited only by the size of the ion source vacuumchamber and travel limits of the x-y table on which the sample receivingstage is mounted. It should be understood that smaller or larger numbersof distinguishable sample positions may thus be defined on samplereceiving surfaces of other geometries.

In a preferred embodiment as illustrated in FIG. 1, a ferromagneticmaterial handle 20 is attached along one edge of the plate on the bottomside, i.e., the side opposite the receiving surface for the samples.This handle 20 may have a rectilinear cross-sectional configuration, andis used to engage an electromagnetic device for the purpose oftransporting the sample plate between component system.

The sample plate 10 has beveled comers corners 22 yet provides a totalsquare surface having 50 mm sides interior of the beveled comers cornerson the top surface of the plate 10 for receiving multiple samples.Samples may be deposited on this plate in a variety of ways, and forexplanation purposes it may be assumed that an array of circular spots16 is photoetched into the plate 10 along with identifying numbers. Thisarrangement easily accommodates up to 1024 sample spots each 1 mm indiameter in a 32×32 array without identifying numbers. Each of these1024 sample spots will accommodate about 100 nanoliters of samplesolution.

As shown in FIG. 2, the samples alternatively may be deposited on theends 24 of removable pins 26, and the pins locked into a two dimensionalarray using a sample holder positioned on a sample plate 10A. A suitableholder 28 may have a rectangular horizontal cross-section, and may besized to receive a 5×5 array of vertical pins. Samples of interest arethus deposited in known locations or spots on the surface of the sampleholder. In other cases, the locations of samples of interest may not beof particular significance. For example, a system may be employed withsamples deposited by blotting from a two-dimensional gel, in which casesamples of interest may be distributed in an unknown pattern over thesample surface.

As shown in FIG. 1, the sample plate 10 has two or more preciselylocated holes 14A, 14B and 14C each located near an edge of the plate10. These holes 14 locate the sample holder when installed in the samplereceiving stage in the ion source of the mass spectrometer and in thesample transport trays. The magnetic material bar 20 may be engaged byan energized electromagnet (not shown) to assist in transporting thesample holder into the sample receiving stage, as discussedsubsequently.

2. Identification of Sample Position and Plate

The x-y coordinate of each sample position on one side (typically thetop side) of the sample plate may be used to determine a unique sampleposition on each sample plate. The diameter of a sample spot centered oneach position may be used to further define a sample position. Theminimum data required to uniquely identify a sample position is the x-ycoordinate and the diameter of the spot. As discussed above, the sampleposition may be further defined by a photoetched well or photoplatedspot centered at the corresponding x-y coordinate on the sample plate,and may be even further defined by the corresponding number etched orplated near the corresponding sample spot.

Each particular sample plate may be identified by a serial number etchedinto the top surface of the plate or attached to or etched into thebottom surface of the plate. A computer readable bar code may be usedwith a sufficient number of digits to uniquely identify the sample platerelative to any other which might be encountered within a series ofsimilar runs. The systems involved in applying the samples to the sampleplates and those for loading the plates into the mass spectrometer asdiscussed below may also be equipped with bar code readers to providethe required identification of the sample plates.

3. Processing and Preparing Samples

The details of this component will depend on the application, the typesof samples to be tested, and the degree to which the samples areprepared and purified prior to being input to the analysis systemdescribed below. The following discussion sets forth the representativesteps required to carry out an automated MALDI analysis. It should beappreciated that additional automated sample preparation andpurification steps could be added. Rate-determining steps may be used,for example, to determine the speed with which the completedetermination can be done.

The invention is particularly suited for DNA sequencing. For thispurpose, it is assumed that a set of sequencing mixtures has beenprepared off-line using either the Maxxam-Gilbert or Sanger method. Themixtures may be presented to the system in the form of liquid solutionsin small vials or tubes in a tray which may be accessed by anautosampler. Substantially the same samples in the same form may bepresented for separation by electrophoresis in conventional DNAsequencing.

With reference to FIG. 3, the sample processing components include anautosampler 40, valve means 42 for controllably adding an appropriatesolution of matrix from containers 44 to each sample, and a pump orother flow system 46 for transferring liquid samples from a selectedsample to a known sample position on the sample plate. The sample plateis precisely located on a holder mounted on a computer-controlled x-ytable 48. Each sample position may be computer recorded at the time thesample aliquot is transferred to the plate. The autosampler may besimilar to autosamplers used with capillary electrophoresis.

FIG. 3 illustrates one embodiment of a suitable system 30 for preparingand processing samples. Samples are presented to the system in standardsample vials, such as small plastic Eppendorf tubes 33. A large numberof samples tubes may be accommodated within a sample input tray 34. Theperson providing the samples enters sample ID information in computer36, selects the dilutions and matrixes required, and sets the internalstandards and relative concentrations, if required, for each sample. Thesystem prepares the requested sample dilutions and matrix and standardadditions, and transfers each sample aliquot to a known position on thesample plate 10 discussed above. The computer 36 generates a data filecontaining sample ID, dilution, matrix, and internal standard (if any)for each position on the sample plate. The sample plate from transporter50 is capable of automatically changing the sample plate when it isfilled, and transporting the filled sample plate to a cassette 54 forsample drying and storage. Each plate is identified with a bar code andboth the sample preparation system and the MALDI instrument are equippedwith bar code readers for automatic sample tracking. Individual sampleplates or cassettes containing up to 20 sample plates may be transferredalong with the sample data to the MALDI instrument for analysis. Thecomputer controlling the sample preparation system is networked with thecomputer (shown in FIG. 8) controlling the mass spectrometer, so thatboth sample information and mass spectral data may be exchanged betweenthe two computers. The samples accordingly may be prepared in onelaboratory and the data processed there, even if the MALDI instrument isin a different location. This feature also allows multiple sampleprocessing and loading stations to be used with a single massspectrometer.

4. Drying and Storing Sample Plates

When each sample location on a plate has been loaded with a sample, thesamples are allowed to dry before the plate is transferred into thevacuum chamber of the mass spectrometer. In the simplest case, theplates may be transferred from the sample loading system to a rack orcassette where they are allowed to dry in laboratory air. In thepreferred embodiment, however, this rack or cassette 54 is locatedinside a sealed chamber 52 equipped with a computer-controlled door 56which allows the samples to be dried in an environment in which thepressure, temperature, and composition of the surrounding atmosphere iscontrolled. In the fully automated mode, each of the loaded and driedsample plates may be transferred from the sample plate storage chamber52 to an adjacent mass spectrometer. Alternatively, the samples may beprepared and loaded off-line onto the sample plates. When a sufficientnumber of sample plates has been loaded with samples, the plurality ofsample plates may be transferred manually to the mass spectrometer andloaded as a complete cassette using the manually operated sample loadingdoor.

5. Transferring Sample Plates into the Mass Spectrometer SampleReceiving Chamber

The manual step involved in loading the sample plates may be eliminatedby adding a sample storage region to the vacuum lock chamber of a massspectrometer, as shown schematically in FIGS. 4 and 5. This provision,when coupled with on-line sample loading, allows the system to beoperated in a fully automatic, unattended mode. In this configuration,an input door 58 is located between the vacuum lock chamber 68 and thestorage chamber 60. An air cylinder transporter 89 equipped withelectromagnets is provided for transporting sample plates 10 from thetransport tray 80 within the storage chamber 60 to the vacuum lockchamber 68. The tray or cassette 80 contains multiple shelves andcorresponding slots each for storing a sample plate. A cassettetransport drive mechanism including a lead screw 64 driven by a steppermotor 66 is provided to allow any selected one of these slots and acorresponding plate 10 in the cassette 80 to be brought into line withtransporter 89.

The system as shown in FIGS. 4 and 5 allows sample plates 10 to beloaded into the storage region of the vacuum lock chamber 68, whileanother sample plate 10 is being analyzed in the ion source chamber 74of a mass spectrometer. In fully automatic operation, whenever a newsample plate 10 may be loaded, the storage chamber 60 is evacuated, theinput door 58 between the storage chamber 60 and the vacuum lock chamber68 is opened, and the new sample plate is automatically moved bytransporter 89 to a sample transport tray 87 provided in the vacuum lockchamber 68. The input door 58 is then closed and the vacuum lock chamber68 remains evacuated. The plate 10 positioned by sample transport tray87 is moved within chamber 68 by an air cylinder transport mechanism 78.

When analysis of the samples on one plate 10 within the ion source iscompleted, the plate 10 is ejected and placed in a vacant slot in thesample storage cassette 80. This cassette 80 is then moved by steppermotor 66 and lead screw 64 to bring a new sample plate in the transporttray 80 in line with the transporter 89, and the new sample plate isloaded. The exchange of samples may thus be accomplished without ventingof the vacuum lock chamber 68, which was evacuated during the time thatthe samples on the previous plate were being analyzed. This allowssample plates to be changed very quickly (at most a few seconds) whilemaintaining the ion source at high vacuum.

The sample storage chamber 60 is equipped with a manually operated door70 through which a number of sample plates loaded with samples that areoff-line can be introduced simultaneously. To load a set of samples, a“manual load” setting is selected on the computer 36. This causes thesample storage chamber 60 to be vented to atmosphere via vent valve 72,and allows the manual load door 70 to be opened. The samples are thenloaded and the chamber evacuated. The entire set of sample plates cannow be analyzed automatically without further operator intervention.

6. Automated Vacuum Lock System

The vacuum lock chamber 68 is equipped with computer controlled valvesand mechanical transport devices which allow the sample plates 10 to betransported under computer control from the sample storage chamber 60(which may be at atmospheric pressure) to the sample receiving stagewithin the evacuated ion source chamber 74 of a mass spectrometer,without venting the evacuated chamber 74. The vacuum lock chamber 68 hasan input port which may be opened or closed by door 58 and through whichsample plates are loaded from the sample storage chamber 60 into thevacuum lock chamber 68. An output port through which a sample plate istransported from the vacuum lock chamber 68 to the ion source vacuumchamber 74 is similarly opened and closed by output door 76. Each doorincludes an “O” ring seal and may be opened and closed by a respectiveair cylinder 75 controlled from the computer 107.

A preferred embodiment of the vacuum lock chamber 68 is depicted in FIG.5 with its associated valves and transporters suitable for fullyautomated operation. A cassette 80 containing a number (typically 20)loaded sample plates 10 may be transferred from either an off-linesample storage chamber or a sample storage chamber 60 attached to thevacuum lock chamber and thus the mass spectrometer. Before loading asample plate 10 into the storage chamber 60 for subsequent analysis bythe mass spectrometer, it may be assumed that the sample loading doors58 and 76 are closed, the vent valve 72 is closed, and the pumpout valve82 connecting the mechanical vacuum pump 85 with the vacuum lock chamber68 is closed. The pumpout valve 86 connecting the mechanical vacuum pump85 with the storage chamber 60 is first opened, thus evacuating thesample storage chamber. When the residual pressure in this chamber 60has reached a predetermined acceptable vacuum level (e.g., 20millitorr), the valve 82 is opened, and the input and output doors 58and 76 are opened, allowing sample plates to be transported between thesample storage chamber 60 and the ion source chamber 74 of the massspectrometer without significantly degrading the vacuum of the massspectrometer. A conventional vacuum pump 96 is provided for maintainingthe chamber 74 at a desired pressure. Once transport of a plate 10 iscomplete, the doors 58 and 76 may be closed by computer control. Thefully automatic operation of the vacuum lock involves the cycle stepswhich begin with completing the measurements on the previous sampleplate, and end with beginning the measurements on the next sample.

A simplified version of the vacuum lock designed for use with remotesample storage chamber is shown schematically in FIGS. 6 and 7. Thissystem is suitable for manually loading individual sample plates intothe mass spectrometer without venting the mass spectrometer vacuumsystem. Prior to loading a sample plate, it may be assumed that theoutput door 76A is closed, and the pumpout valve 82A is closed. The ventvalve 72A is opened allowing the pressure in vacuum lock chamber 92 tobe raised to that of the surrounding atmosphere while the vacuum pump96A attached to the ion source chamber 97 maintains the ion sourcechamber under high vacuum. The input door 98 is then opened and thesample transport tray 99 is transported by its air cylinder 78B throughthe input door 98 to a point where it is accessible for loading. Thesample plates 10 may be manually loaded into the sample transport tray99. Under computer control following a command from the operator, thetray 99 containing a sample plate is retracted into the vacuum lockchamber 92 by air cylinder 78B, and the input door 98 is then closed.The vent valve 72A is then closed, and the pumpout valve 82A is openedand the pump 84A activated until the vacuum lock chamber 92 issufficiently evacuated. When a satisfactory pressure has been reached(typically 50 milliliter), the output door 76A is opened.

With reference now to FIG. 7, the sample plate 10 is then transportedfrom the transport tray 99 to the sample receiving stage, i.e., the ionsource chamber 97, of the mass spectrometer. This transport isaccomplished by energizing a small electromagnet 102 attached to theactuator rod 104 of the air cylinder 89A. When energized, thiselectromagnet 102 engages the strip of magnetic material 20 attached tothe sample plate 10 and firmly holds the plate 10 until the magnet isde-energized. After the sample is in place in the sample receiving stage94 of the mass spectrometer, the magnet 102 is de-energized and thetransport cylinder 89A is retracted, leaving the sample plate 10 in thechamber 97. The output door 76A is then closed and the mass spectrometeris ready for testing the new samples on plate 10. The complete loadingoperation takes less than one minute, and very little gas is introducedinto the ion source vacuum chamber during this operation.

To eject the sample plate and load a new one the process is reversed.First the output door 76A is opened, and the transport cylinder 89Aequipped with the electromagnet 102 is extended so that theelectromagnet makes contact with the magnetic strip on the sample plate10. The electromagnet is energized and the cylinder 89A retracted tomove the sample plate from the ion source chamber 97 to the transporttray 99 in the vacuum lock chamber 92. The output door 76A is closed,the magnet 102 is de-energized, the input door 98 is opened, and thesample tray 99 extended so that the old sample plate can be removed bythe operator and replaced with a new sample plate. Except for this finalstep, the entire operation is accomplished entirely under control ofcomputer 107 with no intervention from the operator except for selectinga “eject” setting on the computer to remove a sample, and an “operate”setting to load a new sample and begin the test.

Operation of the fully automated system shown in FIGS. 4 and 5 is thussimilar to the system shown in FIGS. 6 and 7 except that operatorintervention is minimized in the FIG. 4 system. A preferred systemaccording to this invention combines the features of the systemsdiscussed above. FIG. 8 discloses a system 108 for analyzing a pluralityof samples and includes an additional electromagnetic transporter 89Bwhich transports sample plates from cassette 80A containing vacantsample plates 10 to the sample loading system 30. After loading, thesample plates 10 are transported by transporter 89B to the samplestorage chamber 60. The cassettes discussed above may each hold up to 20sample plates in a vertical stack. The cassette 80 which supplies plates10 to the ion source chamber has at least one empty slot when a sampleplate is being tested in the ion source chamber 74. The position of thiscassette in the storage chamber may be controlled by a computer drivenstepper motor as described above so that any selected slot in thestorage cassette can be brought into the plane defined by the respectivesample plate transporter 89. A tested sample plate may be transportedfrom the ion source chamber to a vacant slot in the cassette within thevacuum lock chamber, and the sample cassette indexed to position anothersample plate for transport from the vacuum lock chamber to the ionsource chamber, then the sample door closed and the new samples on thenew plate tested. While the mass spectrometer is testing one sampleplate, new samples may be manually or automatically loaded and/or testedusing sample plates removed without interfering with the massspectrometer or it vacuum system. Computer 107 controls the massspectrometer and the position of the system components described above.

7. Sequentially Testing Loaded Sample Plates

A preferred embodiment of the ion source 110 and a MALDI massspectrometer 112 is depicted in FIG. 9. A stainless steel block 118 isrigidly mounted to an x-y table 114 via electrically insulating posts116 made of ceramic or polyamide. The block 118 and table 114 may bepositioned within the ion source chamber 74 (or 97) discussed above. Anelectrical potential of up to approximately 30 kV, positive or negative,may be applied to block 118 by a connection to an external power supply115. The x-y position of the block 118 is controlled by one or morestepper motor driven micrometer screws (not shown) conventionally usedwith x-y tables. The block 118 is equipped with standard lip-type guideplates 121 to assist in transporting the sample plate 10 into positionon the face 117 of block 118. Conventional securing members, such asspring loaded balls 119 may be used to cooperate with the holes 14 inthe plate 10 to lock the sample plate into position with respect to theblock 118.

With computer control of the stepper motors, this system allows anyselected point on the sample plate to be positioned precisely (typicallywithin one thousandths of an inch) on the optic axis of the massspectrometer where it is irradiated by the laser beam 136. Beam 136strikes a sample on plate 10 at point 120 within plane 117, resulting inion beam 134. Accordingly ions may be produced from each sample on theplate 10, which is moved automatically by the x-y table 114 betweensample positions with respect to the laser beam.

The remaining components of a suitable time-of-flight mass spectrometer112 as shown in FIG. 9 include a metal plate 124 having a grid hole 122therein, and a metal plate 128 having a grid hole 126 therein. The metalplate 128 may be maintained at ground potential and voltages applied toblock 118 and plate 124 may be varied to set the accelerating electricalpotential desired, which is typically in the range from 15,000 to 50,000volts. A suitable voltage potential between block 118 and plate 124 is10,000 volts, and a suitable voltage potential between plate 124 andplate 128 is from 10,000 to 40,000 volts.

Most of the low weight ions are prevented from reaching the detector 140by deflection plates 130 and 132, which may be spaced 1 cm. apart. Plate130 may be a ground potential. Plate 132 receives a square wave pulsetimed as a function of the laser beam striking a particular sample. Eachpulse thus suppresses low mass ions, so that substantially only desiredions reach the detector 140. Other details with respect to a suitablespectrometer are disclosed in U.S. Pat. Nos. 5,045,694 and 5,160,840.

8. Automatically Adjusting Laser Intensity and Sample Position

In MALDI, the intensity and quality of the mass spectra generated isstrongly dependent on the intensity of the plume of ionized and neutralmaterial that is produced by the incident laser pulse impinging on thesample and matrix. This intensity depends on the laser intensity, thecomposition of the matrix used, and details of the crystalline structureof the matrix and sample on the surface. While it is possible toestablish a narrow range of laser intensities which produce acceptablespectra, one typically cannot predict with the desired precision thelaser intensity which will yield the best results on a particularsample. In general, if the laser intensity if too high, thesignal-to-noise ratio may be excellent, but the mass resolution and massaccuracy is degraded. Conversely, if the laser intensity is too low, themass resolution and accuracy are satisfactory, but the signal level islow and signal-to-noise ratio is poor. Also, the surfaces of multiplesamples on a plate tend to be non-uniform, so that some locations yieldexcellent results and others do not. Under manual control of the laserbeam and sample position, it is possible through a process of trial anderror to find a combination of laser intensity and sample position whichprovides excellent results.

An automatic control used according to this invention closely mirrorswhat is generally the most successful strategy when operating manually.The intensity of the beam output 136 from the laser source 148 isincreased until the ion signal suddenly appears at a relatively highsetting. At this point, signal-to-noise is excellent, but resolution ispoor. As the laser intensity is decreased, the signal may actuallyincrease at first (sometimes going into saturation), but at some lowerintensity the signal is decreased, and the resolution is dramaticallyincreased. With an improved attenuator 138, this hysteresis appears tobe entirely related to changes in the sample properties, and is not dueto hysteresis in the attenuator. The upper and lower values for theseevents are very reasonably reproducible and appear to depend primarilyon the particular matrix used, and only weakly on the samplepreparation, source voltage, or other parameters.

The strategy for exploiting these observations in the automatic modefollows. The upper and lower limits in the acquisition set-up menu andthe laser step size are established. Two choices are provided for thenumber of spectra to be averaged: an upper number and a lower number.The upper number of spectra are averaged when the laser beam 136 is atits maximum intensity, and the lower number is used at all other laserintensities.

When a new sample is selected by the autosampler menu, the acquisitionstarts with the laser beam 136 set at the upper limit. The number ofspectra requested is averaged. If a spectrum acquired contains intensitywithin the desired mass and intensity limits set, the spectrum is savedand calibrated using the upper calibration file associated with thisset-up file. If the spectrum acquired is too intense, i.e., the maximumintensity within the mass window is greater than the upper intensitylevel (typically set just below saturation), the laser intensity isdecreased by one increment and the process repeated until a spectrummeeting the selection criteria is obtained or the lower limit isreached. If the spectrum is too weak, i.e., the maximum intensity withinthe mass window is too weak, the sample is incremented to a new spot andthe process is repeated. If a spectrum is obtained which has intensitywithin the chosen limits at any laser intensity other than the lowerlimit, that spectrum is saved as an upper intensity spectrum and theupper calibration file associated with the acquisition set-up file isused. If an acceptable spectrum is obtained at the lower limit of laserintensity, that spectrum is saved as a lower intensity spectrum and thelower calibration file associated with the acquisition set-up file isused. If both an upper and a lower intensity spectrum are obtained onthe selected sample spot, the acquisition proceeds to the next sample.If only one of these is obtained, or neither one, the sample isincremented to a new spot until both an upper and a lower spectrum havebeen saved, or until the range of possible sample spots has beenexhausted.

9. Automatically Calibrating the Mass Axis

During automatic operation of the MALDI instrument, an automaticprocedure may be used for checking the calibration of and recalibratingthe mass scale to maintain the desired mass accuracy. This can beaccomplished by loading a sample plate containing one or more knownsamples so that the known mass spectrum can be used to automaticallycheck and correct the mass scale as necessary.

The procedure for calibrating the mass axis is described below. Eachacquisition set-up file must have both an upper and a lower calibrationfile associated with it. These files may be chosen from a list of filesalready in existence by the operator preparing the set-up file, or maybe generated using the “calibrate” selection in the set-up file forcalibration based on a selected known sample. Each calibration filewhich is saved may have all of the parameters associated with itsgeneration saved, so that in the event the operator chooses acalibration file which employs different parameter values, a warning isgiven and the acquisition set-up file corresponding to the one that wasused may be displayed with the parameters highlighted that are differentfrom those which have been selected in the new acquisition set-up. Theoperator has the option of approving the chosen calibration file whichis then associated with the new set-up file, even if some parameters aredifferent. Alternatively, the operator may reject the chosen calibrationfile, return to the set-up file, and either choose a differentcalibration file or generate a new one. If a new calibration file isgenerated using a particular set-up file, a “check replace” selectionmay be employed to determine if the file is to replace a pre-existingcalibration file. A new designation for upper or lower calibrationnumbers is also an option.

In addition to the above changes in the manual calibration procedure, anautomatic calibration mode may be used. Particular samples on the sampleplate may be identified as calibration samples, and the calibrationcompound selected from a list. For each sample or calibration compound,the matrix from a list may be selected. For each calibration compoundand matrix combination chosen, a list of masses and laser intensitiesmay be stored. The normally used mass and intensity valves values may beentered as an initial equipment set-up. A service technician will beable to alter initial factory data at the location of the customer.

During automatic calibration, the procedure for acquiring thecalibration spectrum is the same as for acquiring data from a sample. Ifthe calibration designation is selected in the autosampler set-up, thatsample is treated as a calibration sample and the spectrum obtained iscompared to that expected from the reference file. If peaks are foundwithin the default values of mass and internally (typically set by theservice technician), the calibration file for the particular acquisitionset-up and laser intensity being used is recomputed, and the old filereplaced by the new file. If the observed spectrum falls outside thedefault limits, a warning message is momentarily displayed and thenstored for later display when the data are processed. If the attemptedcalibration does not succeed, the old value is retained, and automaticacquisition proceeds. For instrument service purposes, it may bedesirable to retain the old calibration files in a directory accessibleto the service technician.

To implement the above, columns may be added to the autosampler set-upmenu. These columns might include a choice of sample or calibrant, achoice of matrices from a pull-down list, and a pull-down menu showingthe list of known calibrants. The operator may also enter new parameterscharacterizing a new calibrant within another column. The operator mayalso have the option of designating a matrix choice in the acquisitionset-up file.

10. Automatically Interpreting the MALDI Mass Spectra

Mass spectra interpretation depend on the type of samples analyzed andthe information required. The first step is to convert the observedtime-of-flight spectrum into a mass spectrum, i.e., a table of massesand intensities for all of the peaks observed in the time-of-flightspectra. Peaks that are known to be due to the matrix or otherextraneous material will normally be deleted from this list. This massspectrum is obtained by calculating the centroid and integral intensityof each peak. The peak width may also be included (e.g., full width athalf maximum) to provide a measure of the maximum uncertainty in themass determination.

In the application to DNA sequencing, each set of four samples consistsof one sample ending, so that all possible fragments ending in aspecific base are included in each sample set. Accordingly, for each DNAfragment to be sequenced, there is a sample with all possible fragmentsterminating in C, T, A, and G, respectively. Each of these fragments isobserved as a peak in the time-of-flight spectrum of that sample. Bysuperimposing the four spectra, the sequence of bases can be readdirectly. Furthermore, the mass difference between any pair of peaks inthese four spectra mass correspond to the total mass associated with thenucleotides in that portion of the sequence. This provides a significantredundancy in the results, which may be useful for analysis other thanthat involving the simple ordering of the peaks, a feature which is notavailable in electrophoresis. If a peak is very weak and is missed, orif two peaks are insufficiently resolved, a base may be missed by simpleordering. The mass difference observed between the next pair of adjacentpeaks will thus show the error and allow correction. The computer maythus interpret the spectra and directly produce the sequence of bases inthe DNA fragment. If there are any regions of the spectrum where theresults may be consider considered ambiguous or unreliable, e.g.,because the observed mass differences are inconsistent, those regionsmay be flagged so that the operator may perform either manual study orfurther automated analysis on those regions.

According to the technique of this invention a MALDI mass spectrometeris used rather than electrophoresis separation for DNA sequencing. Untilrecently, the MALDI technique was limited to single-stranded DNAfragments up to about 50 bases in length, but the range has now beenextended to fragments as large as 500 bases in length.

Conventional large-scale sequencing is currently being done at a rateapproaching 1 Mb per year of finished sequence. The cost of sequencingis in the vicinity of one U.S. dollar per base. A rate of 500 Mb peryear is required for the Human Genome Project. A price of 20 cents perfinished base is commensurate with the budget and goals of this project.

At the present stage of development, MALDI analysis of DNA fragments canbe done readily on mixtures containing components less than 50 bases inlength. Recent work suggests that this fragment length can be extended,perhaps as much as one order of magnitude to fragments 500 bases inlength. Large scale sequencing would proceed much more rapidly by thistechnique if the fragments analyzed could be extended significantly. Areasonable goal is to be able to accurately analyze mixtures containingoligimers up to 300 bases in length. The resolution and sensitivity ofpresently available instruments is satisfactory. Even with thelimitations imposed by the short segments, the MALDI technique withapplication of the present invention could be competitive withconventional approaches.

The present invention can readily handle at least 4 samples per minute,which corresponds with 50 base fragments to 50 bases of raw data perminute, since 4 separate samples are required to sequence each segment.A single instrument can run at least 1200 minutes per day to provide60,000 bases per day of raw sequence. This is about 22 Mb/year from asingle instrument. This is raw data, however, and the piercing togetherof fragments from short sequence generated data is likely to requireconsiderable redundancy. Nevertheless, a single instrument, even withthe limitations imposed by short segments, can surpass the total outputof present conventional sequencing. The price for this instrument isabout $200,000, and it should have a useful life of at least 5 years.Total cost for operating and maintaining the instrument (includingamortization) should be less than $100,000/year. If the instrumentproduces 2 Mb of finished sequence/year, this corresponds to 5cents/base. 250 such instruments would be required to provide sequencesat the rate required by the Human Genome Project. If the length of thefragments analyzed can be extended, the speed will increase and the costwill rapidly decrease since less redundancy will be required. If thefragment length was increased to 300 bases, the raw data rate increasesproportionally to about 120 Mb/year. The ratio of this raw rate tofinished data rate should improve dramatically and may approach 50Mb/year for a single instrument. In this case, ten instruments couldprovide the rate required by the Human Genome Project at a cost of 0.2cent per base. Although this rate would not include the cost of samplepreparation and data analysis, the rate and cost of raw sequencedetermination would no longer be the limiting feature.

It should be understood that this invention has been disclosed so thatone skilled in the art may appreciate its feature and advantages, andthat a detailed description of specific components and the spacing andsize of the components is not necessary to obtain that understanding.Many of the individual components of the mass spectrometer areconventional in the industry, and accordingly are only schematicallydepicted. The foregoing disclosure and description of the invention arethus explanatory, and various details in the construction of theequipment are not included. Alternative embodiments and operatingtechniques will become apparent to those skilled in the art in view ofthis disclosure, and such modifications should be considered within thescope of the invention, which is defined by the following claims.

1. A system for analyzing a plurality of samples, comprising: aplurality of portable sample supports each having a sample receivingsurface thereon for accommodating a plurality of samples each at a fixedlocation on each sample support; identification means for identifyingeach sample location of each of the plurality of samples on each of theplurality of sample supports; a mass spectrometer for analyzing each ofthe plurality of samples on each sample support, the mass spectrometerhaving a sample receiving chamber therein for receiving each samplesupport; a laser source for striking each sample on each sample supportwhile within the receiving chamber with a laser pulse to desorb andionize sample molecules; support transfer mechanism for automaticallyinputting and outputting each of the sample supports from the samplereceiving chamber of the mass spectrometer; a powered mechanism movablein both an x direction and a y direction perpendicular to the xdirection within the sample receiving chamber for supporting arespective sample support thereon; a vacuum lock chamber connected tothe sample receiving chamber of the mass spectrometer for receiving thesample supports and for maintaining one or more of the sample supportswithin a vacuum controlled environment while the plurality of samples onanother of the sample supports are struck by laser pulses; and computermeans for recording test data from the mass spectrometer for each of theplurality of samples on the sample supports as a function of theidentification means.
 2. The system as defined in claim 1, furthercomprising; a sample loading mechanism for positioning each of aplurality of liquid samples on the sample receiving surface of each ofthe plurality of sample supports; and a curing chamber for drying eachof the plurality of liquid samples on each of the sample supports toform a plurality of solid samples each positioned on a respective samplesupport.
 3. The system as defined in claim 2, further comprising: samplesupport positioning means for positioning each liquid sample on thesample receiving surface of a respective sample support.
 4. The systemas defined in claim 2, further comprising: a sample preparationmechanism for automatically preparing each of the plurality of liquidsamples for a deposit on a respective sample support.
 5. The system asdefined in claim 4, wherein the sample preparation mechanism includes afirst plurality of containers for receiving respective dilutions and asecond plurality of containers for receiving respective matrixes forpreparing each of the plurality of liquid samples each containing aselected dilution.
 6. The system as defined in claim 5, furthercomprising: valve means responsive to the computer means forautomatically controlling the flow of fluids from the first and secondplurality of containers.
 7. The system as defined in claim 1, furthercomprising: a pump responsive to the computer means for pumping liquidsamples to a respective one of the sample supports.
 8. The system asdefined in claim 7, further comprising: a drying chamber for dryingliquid samples on each of the sample supports to form dried samples. 9.The system as defined in claim 8, further comprising: vacuum means forcontrolling a vacuum within the drying chamber in response to thecomputer means.
 10. The system as defined in claim 1, wherein each ofthe plurality of portable sample supports comprises an electricallyconductive sample plate having a plurality of predetermined samplepositions on the sample receiving surface.
 11. The system as defined inclaim 10, wherein each of the plurality of predetermined positions onthe sample plate includes a well for receiving a respective sample. 12.The system as defined in claim 11, wherein each of the plurality ofwells on the sample plate are arranged in one of a plurality of rows andin one of a plurality of columns.
 13. The system as defined in claim 1,wherein: the identification means includes a marking on each samplesupport for identifying each of the plurality of samples on the samplereceiving surface.
 14. The system as defined in claim 1, wherein asample support includes a magnetic handle for cooperating with thesupport transfer mechanism to position the sample support.
 15. Thesystem as defined in claim 1, wherein each of the plurality of samplesupports includes a sample holder and a plurality of pins each removablypositionable with respect to the sample holder, each of the plurality ofpins having a sample receiving surface thereon for receiving arespective one of the plurality of samples.
 16. The system as defined inclaim 1, wherein each of the plurality of sample supports has one ormore locating members for precisely positioning the sample support. 17.The system as defined in claim 1, wherein each of the sample supportscomprises in excess of 80 determined sample positions on the samplereceiving surface.
 18. The system as defined in claim 1, furthercomprising: sample support identification means for identifying each ofthe plurality of sample supports and for inputting sample supportidentification information to the computer means.
 19. The system asdefined in claim 1, further comprising: a sample storage chamber forstoring one or more of the plurality of sample supports; and a poweredtransporter for transporting each of the plurality of sample supportsfrom the sample storage chamber to the vacuum lock chamber.
 20. Thesystem as defined in claim 19, wherein the powered transporter isautomatically responsive to the computer means.
 21. The system asdefined in claim 19, further comprising: a transport cassette forsupporting a plurality of sample supports each in a preselected positionwithin the sample storage chamber.
 22. The system as defined in claim21, further comprising: a transport drive mechanism for selectivelypositioning the transport cassette within the sample storage chamber.23. The system as defined in claim 22, wherein the transport drivemechanism is powered in response to the computer means.
 24. The systemas defined in claim 23, wherein the transport drive mechanism comprisesa lead screw and a stepper motor.
 25. The system as defined in claim 1,further comprising: a door member for selectively controllingcommunication between the vacuum lock chamber and the sample receivingchamber of the mass spectrometer.
 26. The system as defined in claim 25,further comprising: a sample storage chamber for storing one or more ofthe plurality of sample supports; and another door member forcontrolling communication between vacuum lock chamber and the samplestorage chamber.
 27. The system as defined in claim 1, furthercomprising: a pump for selectively evacuating the vacuum lock chamber.28. The system as defined in claim 1, wherein: each of the plurality ofsample supports is moveable between the vacuum lock chamber and thereceiving chamber of the mass spectrometer; and a transporter for movingone of the plurality of samples supports within the vacuum lock chamberwhile the plurality of samples on another of the sample supports arebeing struck with laser pulses.
 29. The system as defined in claim 1,further comprising: a powered sample support transporter for moving oneor more of the plurality of sample supports within the vacuum lockchamber.
 30. The system as defined in claim 1, further comprising: avent valve for selectively venting the vacuum lock chamber toatmospheric pressure.
 31. The system as defined in claim 1, wherein thesupport transfer mechanism is responsive to the computer means.
 32. Thesystem as defined in claim 1, wherein the support transfer mechanismincludes a fluid cylinder and an actuator rod extending between thefluid cylinder and a respective sample support.
 33. The system asdefined in claim 1, wherein: each of the plurality of sample supportsincludes an electromagnet secured thereto; and power to eachelectromagnet is controlled in response to the computing means.
 34. Thesystem as defined in claim 1, wherein the x-y mechanism is an x-y tableresponsive to the computer means.
 35. The system as defined in claim 1,further comprising: an electrically conductive block within the samplereceiving chamber for receiving a respective sample support; and one ormore insulating members electrically insulating the powered positioningmechanism from the electrically conductive block.
 36. The system asdefined in claim 35, further comprising: a securing mechanism fortemporarily affixing the position of a respective sample support withrespect to the electrically conductive block.
 37. The system as definedin claim 1, further comprising: an attenuator for adjusting theintensity of a laser beam output from the laser source.
 38. The systemas defined in claim 37, wherein the attenuator is responsive to thecomputer means.
 39. The system as defined in claim 1, where the computermeans interprets test data from the mass spectrometer.
 40. A system foranalyzing a plurality of samples, comprising: a plurality of portablesample supports each having a sample receiving surface thereon foraccommodating a plurality of samples each at a fixed location on eachsample support; sample identification means for identifying each samplelocation of each of the plurality of samples on each of the plurality ofsample supports; support identification means for identifying each ofthe plurality of sample supports; and a mass spectrometer for analyzingeach of the plurality of samples on a respective one of the samplesupports, the mass spectrometer having a sample receiving chambertherein for receiving a respective sample support; a laser source forstriking each sample on each sample support while within the receivingchamber with a laser pulse to desorb and ionize sample molecules;support transfer mechanism for automatically inputting and outputtingeach of the sample supports from the sample receiving chamber of themass spectrometer; a vacuum lock chamber connected with the samplereceiving chamber of the mass spectrometer for receiving each of thesample supports and for maintaining one or more of the sample supportswithin a vacuum controlled environment while the plurality of samples onanother of the sample supports are struck by laser pulses; a samplestorage chamber for storing one or more of the plurality of samplesupports; a powered transporter for transporting each of the pluralityof sample supports from the sample storage chamber to the vacuum lockchamber; and computer means for controlling the support transfermechanism and for receiving information from the sample identificationmeans and the support identification means for recording test data fromthe mass spectrometer for each of the plurality of samples on each ofthe sample supports.
 41. The system as defined in claim 40 furthercomprising; a sample loading mechanism for positioning each of aplurality of liquid samples on the sample receiving surface of each ofthe plurality of sample supports; and a curing chamber for drying eachof the plurality of liquid samples on each of the sample supports toform a plurality of solid samples each positioned on a respective samplesupport.
 42. The system as defined in claim 40, further comprising: apump responsive to the computer means for pumping liquid samples to arespective one of the sample supports.
 43. The system as defined inclaim 40, wherein each of the plurality of portable sample supportscomprises an electrically conductive sample plate having a plurality ofpredetermined sample positions on the sample receiving surface.
 44. Thesystem as defined in claim 40, wherein: the sample identification meansincludes a marking on each sample support for identifying each of theplurality of samples on the sample receiving surface.
 45. The system asdefined in claim 40, wherein a sample support includes a magnetic handlefor cooperating with the support transfer mechanism to position thesample support.
 46. The system as defined in claim 40, wherein each ofthe plurality of sample supports includes a sample holder and aplurality of pins each removably positionable with respect to the sampleholder, each of the plurality of pins having a sample receiving surfacethereon for receiving a respective one of the plurality of samples. 47.The system as defined in claim 40, wherein each of the plurality ofsample supports has one or more locating members for preciselypositioning the sample support.
 48. The system as defined in claim 40,wherein each of the sample supports comprises in excess of 80 determinedsample positions on the sample receiving surface.
 49. The system asdefined in claim 40, wherein the powered transporter is automaticallyresponsive to the computer means.
 50. The system as defined in claim 40,further comprising: a transport cassette for supporting a plurality ofsample supports each a preselected position.
 51. The system as definedin claim 50, further comprising: a transport drive mechanism forselectively positioning the transport cassette within the storagechamber; and the transport drive mechanism being powered in response tothe computer means.
 52. The system as defined in claim 40, furthercomprising: a door member for selectively controlling communicationbetween the vacuum lock chamber and the sample receiving chamber of themass spectrometer.
 53. The system as defined in claim 52, furthercomprising: another door member for controlling communication betweenvacuum lock chamber and the sample storage chamber.
 54. The system asdefined in claim 40, further comprising: a powered sample supporttransporter for moving one or more of the plurality of sample supportswithin the vacuum lock chamber.
 55. The system as defined in claim 40,wherein the support transfer mechanism includes a fluid cylinder and anactuator rod extending between the fluid cylinder and a respectivesample support.
 56. The system as defined in claim 40, wherein: each ofthe plurality of sample supports includes an electromagnet securedthereto; and power to each electromagnet is controlled in response tothe computing means.
 57. The system as defined in claim 40, furthercomprising: powered positioning mechanism for selectively positioningeach of the plurality of sample supports within the sample receivingchamber.
 58. The system as defined in claim 57, further comprising: thepowered positioning mechanism is an x-y table responsive to thecomputing means; an electrically conductive block within the samplereceiving chamber for receiving a respective sample support; and one ormore insulating members electrically insulating the powered positioningmechanism from the electrically conductive block.
 59. The system asdefined in claim 40, further comprising: an attenuator responsive to thecomputer means for adjusting the intensity of a laser beam output fromthe laser source.
 60. A method of analyzing a plurality of sampleswithin a sample receiving chamber of a mass spectrometer, the methodcomprising: supporting each of a plurality of samples at a fixedlocation on one of a plurality of sample supports; identifying eachsample location of each of the plurality of samples on each of theplurality of sample supports; providing a vacuum lock chamber forreceiving the sample supports and for maintaining one or more of thesample supports within a vacuum controlled environment while theplurality of samples on another of the sample supports are struck bylaser pulses; automatically inputting and outputting each of the samplesupports from the sample receiving chamber of the mass spectrometer tothe vacuum lock chamber; moving each sample support within the samplereceiving chamber in both an x direction and a y direction perpendicularto the x direction; striking each sample on each sample support whilewithin the receiving chamber with a laser pulse to desorb and ionizesample molecules; and recording test data in a computer from the massspectrometer for each of the plurality of samples on the sample support.61. The method as defined in claim 60, further comprising: positioningeach of a plurality of liquid samples on the sample receiving surface ofeach of the plurality of sample supports; and drying each of theplurality of liquid samples on each of the sample supports to form aplurality of solid samples each positioned on a respective samplesupport.
 62. The method as defined in claim 61, further comprising:automatically preparing each of the plurality of liquid samples fordeposit on a respective sample support.
 63. The method as defined inclaim 60, further comprising: arranging each of the plurality of samplesin each sample support in a plurality of rows and in a plurality ofcolumns.
 64. The method as defined in claim 60, wherein the step ofidentifying includes: marking each sample support for identifying eachof the plurality of samples.
 65. The method as defined in claim 60,further comprising: forming in excess of 80 predetermined samplepositions on each of the respective sample supports.
 66. The method asdefined in claim 60, further comprising: storing one or more of theplurality of sample supports within a sample storage chamber; andautomatically transporting each of the plurality of sample supports fromthe sample storage chamber to the vacuum lock chamber in response to thecomputer.
 67. The method as defined in claim 60, further comprising:supporting each of the plurality of sample supports at a preselectedposition within a transport cassette.
 68. The method as defined in claim60, further comprising: selectively positioning the transport cassettein response to the computer.
 69. The method as defined in claim 60,further comprising: controlling communication from within the vacuumlock chamber to the environment exterior of the vacuum lock chamber inresponse to the computer.
 70. The method as defined in claim 60, furthercomprising: moving a sample support with the vacuum lock chamber whilethe plurality of samples on another of the sample supports are beingstruck with laser pulses.
 71. The method as defined in claim 60, furthercomprising: controlling an x-y table in response to the computer forpositioning the plurality of samples within the sample receiving chamberof the mass spectrometer.
 72. The method as defined in claim 71, furthercomprising: supporting each of the plurality of sample supports on anelectrically conductive block within the sample receiving chamber; andelectrically insulating the x-y table from the electrically conductiveblock.
 73. The method as defined in claim 72, further comprising:temporarily affixing the position of a respective sample support withrespect to the electrically conductive block.
 74. The method as definedin claim 60, further comprising: adjusting the intensity of a laser beamoutput from the laser source in response to the computer.
 75. A systemfor obtaining mass data comprising: a mass spectrometer comprising anion source chamber, wherein the ion source chamber comprises a samplereceiving stage adapted to support a sample support, and a mechanism tomove the sample receiving stage in an x direction and in a y directionperpendicular to the x direction, wherein the x direction and the ydirection lie substantially in the same plane; a laser source in opticalcommunication with the ion source chamber, wherein the laser source isadapted to provide a laser pulse to a sample support in the ion sourcechamber; a vacuum lock chamber connected with the ion source chamber,wherein the vacuum lock chamber comprises a sample support holderadapted to support more than one sample support; and a sample supporttransfer mechanism adapted to: (a) disassociate a first sample supportfrom the sample receiving stage, transport the first sample support fromthe ion source chamber through an output port to the vacuum lock chamberand to associate the first sample support with the sample supportholder; and (b) disassociate a second sample support from the samplesupport holder, transport the second sample support from the vacuum lockchamber through the output port to the ion source chamber and toassociate the second sample support with the sample receiving stage. 76.The system of claim 75 further comprising an electronic controlmechanism to control at least the mechanism to move the sample receivingstage.
 77. The system of claim 76 wherein the electronic controlmechanism comprises a computer.
 78. The system of claim 75 wherein thelaser source is adapted to provide a laser pulse to irradiate a sampleon a sample support.
 79. The system of claim 75 wherein the samplesupport holder comprises a cassette adapted to hold a plurality ofsample supports.
 80. The system of claim 75 further comprising a samplesupport.
 81. The system of claim 80 wherein the sample support comprisesa plurality of samples each disposed at fixed locations on the samplesupport.
 82. The system of claim 81 wherein the sample support furthercomprises a location identifier associated with at least one of thefixed locations.
 83. The system of claim 75 further comprising a doormember positioned between the ion source chamber and the vacuum lockchamber.
 84. The system of claim 75 further comprising a vacuum pumpindependently associated with the vacuum lock chamber.
 85. The system ofclaim 75 further comprising a sample preparation system associated withthe vacuum lock chamber, wherein the sample preparation system isadapted to deliver a plurality of samples to a sample support prior tointroduction to the vacuum lock chamber.
 86. The system of claim 85wherein the sample preparation system comprises a sample loadingmechanism adapted to position each of a plurality of liquid samples on asample support.
 87. The system of claim 86 wherein the samplepreparation system further comprises a sample curing chamber to dry eachof the plurality of liquid samples on a sample support.
 88. A system forobtaining mass data comprising: a mass spectrometer comprising an ionsource chamber, wherein the ion source chamber comprises a samplereceiving stage adapted to support a sample support, and a mechanism tomove the sample receiving stage; a laser source in communication withthe ion source chamber, wherein the laser source is adapted to provide alaser pulse to a sample support in the ion source chamber; a vacuum lockchamber connected with the ion source chamber; a sample storage chamberconnected to the vacuum lock chamber, wherein the sample storage chambercomprises a sample support holder adapted to support at least one samplesupport; and a sample support transfer mechanism adapted to: (a)disassociate a first sample support from the sample receiving stage,transport the first sample support from the ion source chamber throughan output port to the vacuum lock chamber and to associate the firstsample support with the sample support holder; and (b) disassociate asecond sample support from the sample support holder, transport thesecond sample support from the vacuum lock chamber through the outputport to the ion source chamber and to associate the second samplesupport with the sample receiving stage.
 89. The system of claim 88wherein the mechanism to move the sample receiving stage is adapted tomove the sample receiving stage in an x direction and in a y directionperpendicular to the x direction.
 90. A method of obtaining mass datacomprising the steps of: supporting each of a plurality of samples at afixed location on one of a plurality of sample supports; providing anion source chamber having a sample receiving stage adapted to support asample support; providing a vacuum lock chamber adapted to maintain oneor more of the sample supports within a vacuum controlled environmentwhile a sample on another of the sample supports is struck by a laserpulse, wherein the vacuum lock chamber comprises a sample support holderadapted to receive the plurality of sample supports; moving a firstsample support associated with the sample receiving stage within the ionsource chamber in an x direction and in a y direction perpendicular tothe x direction; striking with a laser pulse a desired number of theplurality of samples on the first sample support within the ion sourcechamber to desorb and ionize sample molecules; disassociating the firstsample support from the sample receiving stage; transporting the firstsample support from the ion source chamber to the vacuum lock chamber;associating the first sample support with the sample support holder;disassociating a second sample support from the sample support holder;transporting the second sample support from the vacuum lock chamber tothe ion source chamber; associating the second sample support with thesample receiving stage; moving the second sample support associated withthe sample receiving stage within the ion source chamber in an xdirection, and in a y direction perpendicular to the x direction; andstriking with a laser pulse a desired number of the plurality of sampleson the second sample support within the ion source chamber to desorb andionize sample molecules.
 91. The method of claim 90 wherein the vacuumlock chamber and ion source chamber are in fluid communication and aremaintained under a vacuum controlled environment during thedissociating, transporting, and associating of the first and secondsample supports.
 92. The method of claim 90 further comprising the stepof: recording in a computer mass data corresponding to at least one ofthe plurality of samples struck with a laser pulse.
 93. A system forobtaining mass data comprising: a mass spectrometer comprising an ionsource chamber, wherein the ion source chamber comprises a samplereceiving stage adapted to support a sample support, and a mechanism tomove the sample receiving stage in an x direction and in a y directionperpendicular to the x direction, wherein the x direction and the ydirection lie substantially in the same plane; a laser source in opticalcommunication with the ion source chamber, wherein the laser source isadapted to provide a laser pulse to a sample support in the ion sourcechamber; a vacuum lock chamber connected with the ion source chamber,wherein the vacuum lock chamber comprises a sample support holderadapted to support more than one sample support; a sample supporttransfer mechanism adapted to: (a) disassociate a first sample supportfrom the sample receiving stage, transport the first sample support fromthe ion source chamber to the vacuum lock chamber and to associate thefirst sample support with the sample support holder; and (b)disassociate a second sample support from the sample support holder,transport the second sample support from the vacuum lock chamber to theion source chamber and to associate the second sample support with thesample receiving stage; and means for maintaining the vacuum lockchamber and the ion source chamber in fluid communication and under avacuum controlled environment during disassociation, transportation andassociation of the first and second sample supports.
 94. A system forobtaining mass data comprising: a mass spectrometer comprising an ionsource chamber, wherein the ion source chamber comprises a samplereceiving stage adapted to support a sample support, and a mechanism tomove the sample receiving stage; a laser source in communication withthe ion source chamber, wherein the laser source is adapted to provide alaser pulse to a sample support in the ion source chamber; a vacuum lockchamber connected with the ion source chamber; a sample storage chamberconnected to the vacuum lock chamber, wherein the sample storage chambercomprises a sample support holder adapted to support at least one samplesupport; a sample support transfer mechanism adapted to: (a)disassociate a first sample support from the sample receiving stage,transport the first sample support from the ion source chamber to thevacuum lock chamber and to associate the first sample support with thesample support holder; and (b) disassociate a second sample support fromthe sample support holder, transport the second sample support from thevacuum lock chamber to the ion source chamber and to associate thesecond sample support with the sample receiving stage; and means formaintaining the vacuum lock chamber and the ion source chamber in fluidcommunication and under a vacuum controlled environment duringdisassociation, transportation and association of the first and secondsample supports.